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Tsang CTT, Hui TKL, Chung NM, Yuen WT, Tsang LM. Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification. Mol Ecol 2024; 33:e17377. [PMID: 38713089 DOI: 10.1111/mec.17377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/08/2024]
Abstract
The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont.
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Affiliation(s)
- Chandlar Tsz To Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tom Kwok Lun Hui
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nga Man Chung
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing Tan Yuen
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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Béziat NS, Duperron S, Gros O. Environmental Transmission of Symbionts in the Mangrove Crabs Aratus pisonii and Minuca rapax: Acquisition of the Bacterial Community through Larval Development to Juvenile Stage. Microorganisms 2024; 12:652. [PMID: 38674597 PMCID: PMC11052079 DOI: 10.3390/microorganisms12040652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 04/28/2024] Open
Abstract
Aratus pisonii and Minuca rapax are two brachyuran crabs living with bacterial ectosymbionts located on gill lamellae. One previous study has shown that several rod-shaped bacterial morphotypes are present and the community is dominated by Alphaproteobacteria and Bacteroidota. This study aims to identify the mode of transmission of the symbionts to the new host generations and to identify the bacterial community colonizing the gills of juveniles. We tested for the presence of bacteria using PCR with universal primers targeting the 16S rRNA encoding gene from gonads, eggs, and different larval stages either obtained in laboratory conditions or from the field. The presence of bacteria on juvenile gills was also characterized by scanning electron microscopy, and subsequently identified by metabarcoding analysis. Gonads, eggs, and larvae were negative to PCR tests, suggesting that bacteria are not present at these stages in significant densities. On the other hand, juveniles of both species display three rod-shaped bacterial morphotypes on gill lamellae, and sequencing revealed that the community is dominated by Bacteroidota and Alphaproteobacteria on A. pisonii juveniles, and by Alphaprotobacteria, Bacteroidota, and Acidimicrobia on M. rapax juveniles. Despite the fact that juveniles of both species co-occur in the same biotope, no shared bacterial phylotype was identified. However, some of the most abundant bacteria present in adults are also present in juveniles of the same species, suggesting that juvenile-associated communities resemble those of adults. Because some of these bacteria were also found in crab burrow water, we hypothesize that the bacterial community is established gradually during the life of the crab starting from the megalopa stage and involves epibiosis-competent bacteria that occur in the environment.
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Affiliation(s)
- Naëma Schanendra Béziat
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Campus de Fouillole, 97110 Pointe-à-Pitre, France;
- Caribaea Initiative, Université des Antilles, 97110 Pointe-à-Pitre, France
| | - Sébastien Duperron
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d’Histoire Naturelle, UMR 7245, CNRS, 57 Rue Cuvier (CP54), 75005 Paris, France;
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Campus de Fouillole, 97110 Pointe-à-Pitre, France;
- C3MAG, UFR des Sciences Exactes et Naturelles, Université des Antilles, 97110 Pointe-à-Pitre, France
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Chen M, Su S, Zhang C, Zhu J, Feng W, Chen H, Jiang J, Lu Z, Liu W, Gan J. The Role of Biogeography in Shaping Intestinal Flora and Influence on Fatty Acid Composition in Red Swamp Crayfish (Procambarus clarkii). MICROBIAL ECOLOGY 2023; 86:3111-3127. [PMID: 37878052 DOI: 10.1007/s00248-023-02298-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/30/2023] [Indexed: 10/26/2023]
Abstract
Intestinal microbiota plays an important role in promoting digestion, metabolism, and immunity. Intestinal microbiota and fatty acids are important indicators to evaluate the health and nutritional composition of Procambarus clarkii. They have been shown to be strongly influence by environmental and genetic factors. However, it is not clear whether environmental factors have a greater impact on the intestinal microbiota and fatty acid composition of crayfish. The link between the intestinal microbial communities and fatty acid (FA) compositions of red swamp crayfish from different geographical has not yet been studied. Thus, the current paper focuses on the influence of different environments on the fatty acids in muscles of crayfish and the possible existence between gut microbiota and fatty acids. Therefore, in this study, we compared the fatty acid compositions and intestinal microbiota of five crayfish populations from different geographical locations. The results were further analyzed to determine whether there is a relationship between geographical location, fatty acid compositions and intestinal microbiota. The gut microbial communities of the crayfish populations were characterized using 16S rRNA high-throughput gene sequencing. The results showed that there were significant differences in FA compositions of crayfish populations from different geographical locations. A similar trend was observed in the gut microbiome, which also varied significantly according to geographic location. Interestingly, the analysis revealed that there was a relationship between fatty acid compositions and intestinal microbes, revealed by alpha diversity analysis and cluster analysis. However, further studies of the interactions between the P. clarkii gut microbiota and biochemical composition are needed, which will ultimately reveal the complexity of microbial ecosystems with potential applications in aquaculture and species conservation.
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Affiliation(s)
- Ming Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Shengyan Su
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Chengfeng Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jian Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenrong Feng
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Huangen Chen
- Jiangsu Fishery Technology Promotion Center, Jiangsu, China
| | - Jingjing Jiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Zeyu Lu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Wenting Liu
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jingchang Gan
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
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Smalls J, Grim C, Parveen S. AssesSments of Vibrio parahaemolyticus and Vibrio vulnificus levels and microbial community compositions in blue crabs ( Callinectes sapidus) and seawater harvested from the Maryland Coastal Bays. Front Microbiol 2023; 14:1235070. [PMID: 37854338 PMCID: PMC10581026 DOI: 10.3389/fmicb.2023.1235070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/01/2023] [Indexed: 10/20/2023] Open
Abstract
Introduction Fluctuations in environmental physicochemical parameters can affect the diversity and prevalence of microbial communities, including vibrios, associated with aquatic species and their surrounding environments. This study aimed to investigate the population dynamics of two Vibrio species as well as the microbial community diversity of whole crab and seawater from the Maryland Coastal Bays (MCBs), using 16S rRNA sequencing. Methods During this study, three crabs and 1 L of seawater were collected monthly from two sites for 3 months. Crab tissue was extracted and pooled for each site. Extracted crab tissue and seawater were analyzed for Vibrio parahaemolyticus and V. vulnificus using Most Probable Number (MPN) real-time PCR. For 16S rRNA microbiome analysis, three different DNA extraction kits were evaluated to extract microbial DNA from individual crabs. Also, 500 mL of each seawater sample was filtered for DNA extraction. Results Results indicated that sample types and sampling periods had a significant effect on the alpha diversity of the microbial community of crabs and seawater (p < 0.05); however, no statistical difference was found between DNA extraction kits. Beta diversity analysis also found that the microbial compositions between sample types and temporal distributions were statistically significant. Taxonomic classification revealed that Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes were present in both crab and seawater samples. Vibrio parahaemolyticus and V. vulnificus were also detected in both crab and seawater samples, although crabs contained a higher concentration of the bacterium compared to the seawater samples. It was found that vibrios were not a dominant species in the microbial community of crab or seawater samples. Discussion Results from this study provide further insight into species diversity and phylogenetic compositions of blue crabs and seawater from the MCBs. These approaches will help in risk assessments that are essential in the overall advancement of public health.
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Affiliation(s)
- Jasmine Smalls
- Department of Agriculture, Food and Resource Sciences, Food and Agricultural Sciences Program, University of Maryland Eastern Shore, Princess Anne, MD, United States
| | - Christopher Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Salina Parveen
- Department of Agriculture, Food and Resource Sciences, Food and Agricultural Sciences Program, University of Maryland Eastern Shore, Princess Anne, MD, United States
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Guillén-Watson R, Arias-Andres M, Rojas-Jimenez K, Wehrtmann IS. Microplastics in feed cause sublethal changes in the intestinal microbiota and a non-specific immune response indicator of the freshwater crayfish Procambarus clarkii (Decapoda: Cambaridae). Front Microbiol 2023; 14:1197312. [PMID: 37533827 PMCID: PMC10390773 DOI: 10.3389/fmicb.2023.1197312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023] Open
Abstract
Microplastics (MP) are a hazardous pollutant of global concern that threatens aquatic ecosystems and public health. We used the invasive, cosmopolitan, and environmentally versatile red swamp crayfish Procambarus clarkii as a model to study the effects of MP on the intestinal microbiome. Crayfish collected from the environment were compared with specimens exposed to recycled Polyethylene terephthalate (rPET) MP in feed (30%) for 96 h in the laboratory and a control group. We analyzed the 16S rRNA of the intestinal bacteria by PCR-DGGE and high-throughput sequencing. MP exposure caused dysbiosis of the intestinal microbiota, with an increase in Alphaproteobacteria and Actinobacteria. We detected higher abundance of opportunistic genera such as Klebsiella, Acinetobacter, Hydromonas, Pseudomonas, Gemmobacter, and Enterobacter on MP fed organisms. Moreover, MP exposure reduced the abundance of Clostridia and Bateroidetes, which are important for immune system development and pathogen prevention. Furthermore, MP exposure decreased the phenoloxidase (PO) immune response in crayfish. There was a significant difference in the richness of intestinal bacterial communities after consumption of food contaminated with MP, likely increasing the abundance of opportunistic bacteria in the intestinal microbiota. Our results suggest that MP alter the gut microbial composition and impair the health of P. clarkii.
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Affiliation(s)
- Rossy Guillén-Watson
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Maria Arias-Andres
- Laboratorio ECOTOX, Instituto Regional de Estudios en Sustancias Tóxicas (IRET), Universidad Nacional, Heredia, Costa Rica
| | | | - Ingo S. Wehrtmann
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET), Universidad de Costa Rica, San José, Costa Rica
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Galván V, Pascutti F, Sandoval NE, Lanfranconi MP, Lozada M, Arabolaza AL, Mac Cormack WP, Alvarez HM, Gramajo HC, Dionisi HM. High wax ester and triacylglycerol biosynthesis potential in coastal sediments of Antarctic and Subantarctic environments. PLoS One 2023; 18:e0288509. [PMID: 37459319 PMCID: PMC10351704 DOI: 10.1371/journal.pone.0288509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/28/2023] [Indexed: 07/20/2023] Open
Abstract
The wax ester (WE) and triacylglycerol (TAG) biosynthetic potential of marine microorganisms is poorly understood at the microbial community level. The goal of this work was to uncover the prevalence and diversity of bacteria with the potential to synthesize these neutral lipids in coastal sediments of two high latitude environments, and to characterize the gene clusters related to this process. Homolog sequences of the key enzyme, the wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) were retrieved from 13 metagenomes, including subtidal and intertidal sediments of a Subantarctic environment (Ushuaia Bay, Argentina), and subtidal sediments of an Antarctic environment (Potter Cove, Antarctica). The abundance of WS/DGAT homolog sequences in the sediment metagenomes was 1.23 ± 0.42 times the abundance of 12 single-copy genes encoding ribosomal proteins, higher than in seawater (0.13 ± 0.31 times in 338 metagenomes). Homolog sequences were highly diverse, and were assigned to the Pseudomonadota, Actinomycetota, Bacteroidota and Acidobacteriota phyla. The genomic context of WS/DGAT homologs included sequences related to WE and TAG biosynthesis pathways, as well as to other related pathways such as fatty-acid metabolism, suggesting carbon recycling might drive the flux to neutral lipid synthesis. These results indicate the presence of abundant and taxonomically diverse bacterial populations with the potential to synthesize lipid storage compounds in marine sediments, relating this metabolic process to bacterial survival.
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Affiliation(s)
- Virginia Galván
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Federico Pascutti
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Natalia E. Sandoval
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Mariana P. Lanfranconi
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Mariana Lozada
- Instituto de Biología de Organismos Marinos (IBIOMAR-CONICET), Puerto Madryn, Chubut, Argentina
| | - Ana L. Arabolaza
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Walter P. Mac Cormack
- Instituto de Nanobiotecnología (NANOBIOTEC-UBA-CONICET), San Martín, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto Antártico Argentino (IAA), San Martín, Buenos Aires, Argentina
| | - Héctor M. Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Hugo C. Gramajo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Hebe M. Dionisi
- Centro para el Estudio de Sistemas Marinos (CESIMAR-CONICET), Puerto Madryn, Chubut, Argentina
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Feng W, Wang M, Dong D, Hui M, Zhang H, Fu L, Zhong Z, Xu Z, Li C. Variation in epibiotic bacteria on two squat lobster species of Munidopsidae. Front Microbiol 2023; 14:1197476. [PMID: 37448572 PMCID: PMC10336205 DOI: 10.3389/fmicb.2023.1197476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 07/15/2023] Open
Abstract
The relationships between epibiotic bacteria on deep-sea hosts and host lifestyle factors are of particular interest in the field of deep-sea chemoautotrophic environmental adaptations. The squat lobsters Shinkaia crosnieri and Munidopsis verrilli are both dominant species in cold-seep ecosystems, and they have different distributions and feeding behaviors. These species may have evolved to have distinct epibiotic microbiota. Here, we compared the epibiotic bacterial communities on the M. verrilli carapace (MVcarapace), S. crosnieri carapace (SCcarapace), and S. crosnieri ventral plumose setae (SCsetae). The epibiotic bacteria on SCsetae were dense and diverse and had a multi-layer configuration, while those on MVcarapace and SCcarapace were sparse and had a monolayer configuration. Chemoautotrophic bacteria had the highest relative abundance in all epibiotic bacterial communities. The relative abundance of amplicon sequence variant 3 (ASV3; unknown species in order Thiotrichales), which is associated with sulfide oxidation, was significantly higher in SCsetae than MVcarapace and SCcarapace. Thiotrichales species seemed to be specifically enriched on SCsetae, potentially due to the synthetic substrate supply, adhesion preference, and host behaviors. We hypothesize that the S. crosnieri episymbionts use chemical fluxes near cold seeps more efficiently, thereby supporting the host's nutrient strategies, resulting in a different distribution of the two species of squat lobster.
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Affiliation(s)
- Wenze Feng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Minxiao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong Dong
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Min Hui
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Huan Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Lulu Fu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhaoshan Zhong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zheng Xu
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Chaolun Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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Bacci G, Fratini S, Meriggi N, Cheng CLY, Ng KH, Pindo M, Iannucci A, Mengoni A, Cavalieri D, Cannicci S. Conserved organ-specific microbial assemblages in different populations of a terrestrial crab. Front Microbiol 2023; 14:1113617. [PMID: 37378290 PMCID: PMC10291174 DOI: 10.3389/fmicb.2023.1113617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Microorganisms are ubiquitous in the environment and provide genetic and physiological functions to multicellular organisms. Knowledge on the associated microbiota is becoming highly relevant to understand the host's ecology and biology. Among invertebrates, many examples of endosymbiosis have been described, such as those in corals, ants, and termites. At present, however, little is known on the presence, diversity, and putative roles of the microbiota associated to brachyuran crabs in relation to their environment. In this work we investigated the associated microbiota of three populations of the terrestrial brachyuran crab Chiromantes haematocheir to find evidence of a conserved organ-specific microbiome unrelated to the population of origin and dissimilar from environmental microbial assemblages. Bacterial 16S rRNA gene and fungal ITS sequences were obtained from selected crab organs and environmental matrices to profile microbial communities. Despite the presence of truly marine larval stages and the absence of a gregarious behaviour, favouring microbiota exchanges, we found common, organ-specific microbiota, associated with the gut and the gills of crabs from the different populations (with more than 15% of the genera detected specifically enriched only in one organ). These findings suggest the presence of possible functional roles of the organ-specific microbiota.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Sara Fratini
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | | | - Ka Hei Ng
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Massimo Pindo
- The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Alessio Iannucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Stefano Cannicci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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Liu C, Liu M, Wang Y, Shi B, Pan D. Insights into the Gut Microbiota of the Freshwater Crab Sinopotamon planum across Three Seasons and Its Associations with the Surrounding Aquatic Microbiota. DIVERSITY 2023. [DOI: 10.3390/d15040519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Gut microbiota is closely related to the health of the host and its adaptation to environmental changes. Sinopotamon planum is a species of freshwater crab that lives in the water for three seasons and plays a key role in freshwater ecosystems as a benthic macroinvertebrate, an important indicator of aquatic ecological health. In this study, we sequenced 60 gut microbial samples of S. planum and nine microbial samples from the surrounding water in spring, summer, and autumn based on the 16S rRNA gene. The results showed that gut microbiota had the highest alpha diversity in summer, which may be related to increased adaptability in summer. Firmicutes, Proteobacteria, and Bacteroidota were the most dominant phyla of gut microbiota across three seasons, with Candidatus Hepatoplasma and Candidatus Bacilloplasma being the main genera. These main phyla and genera may be key to maintaining a stable function of the intestinal environment. Firmicutes was the phylum with the highest relative abundance, which is probably related to the carnivorous behaviour of S. planum. The abundant C. Hepatoplasma may be related to the starvation of S. planum in the wild. In both gut and water microbiota, beta diversity analyses showed significant differences across seasons. Comparative analysis of gut microbes and surrounding water microbes showed significant differences in microbial diversity and composition between gut and surrounding water. In conclusion, the structure of the gut microbial community of S. planum differed significantly between the studied seasons, but the water microbial community around S. planum was less variable and significantly different from the gut microbes. The seasonal differences in gut microbes are more likely the result of self-internal adaptation to changes in water temperature and food resources between seasons.
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Affiliation(s)
- Caixin Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Meijun Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yifan Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Boyang Shi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Da Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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10
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Jiang Y, Han X, Li M, Feng N, Yang P, Zhao H, Zhang C, Shi M, Huang Z, Sun R, Liu S, Hu D. Changes in the gut microbiota of forest musk deer (Moschus berezovskii) during ex situ conservation. Front Microbiol 2022; 13:969593. [PMID: 36160192 PMCID: PMC9493438 DOI: 10.3389/fmicb.2022.969593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Ex situ conservation is an important technique for protecting rare and endangered wildlife, and maintaining stable individual health is crucial to its success. Gut microbiota composition is a critical indicator of animal health and should therefore be closely monitored during ex situ conservation to track impacts on animal health. Forest musk deer (Moschus berezovskii) were historically distributed in Hebei Province, China, however, they are now extinct in the region. Thus, ex situ conservation efforts were conducted in 2016 whereby approximately 50 individuals were artificially migrated from Weinan, Shaanxi to Huailai, Hebei. To monitor gut health of these migrated individuals, we used 16S rRNA high-throughput sequencing technology to examine the microbiota differences between Huailai juvenile and Weinan juvenile groups, and between Huailai adult and Weinan adult groups. Alpha diversity analysis indicated that the richness of microbiota significantly decreased after migration to the Huailai area, and the beta diversity results also showed significant dissimilarity in gut microbial communities, demonstrating the distinct microbial structure differences in the forest musk deer population from the two areas, for both juvenile and adult groups, respectively. In addition, PICRUSt functional profile prediction indicated that the functions of gut digestion and absorption, and degradation of toxic substances were significantly weakened after ex situ conservation. Differences in diet composition between the individuals of the two sites were also observed and the impact of food on gut microbiota compositions within forest musk deer during ex situ conservation was investigated. This study provides a theoretical basis for developing ex situ conservation measures, especially for the protection of forest musk deer.
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Affiliation(s)
- Yuanlin Jiang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiangyu Han
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Mengqi Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Nuannuan Feng
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Pengcheng Yang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Haoxi Zhao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Chenxi Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Minghui Shi
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Zhixin Huang
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd., Zhangzhou, Fujian, China
| | - Rubin Sun
- Huailai Zhiyangtianbao Technical Development Co., Ltd., Zhangjiakou, China
| | - Shuqiang Liu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- *Correspondence: Shuqiang Liu,
| | - Defu Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Defu Hu,
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11
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Zhan M, Xi C, Gong J, Zhu M, Shui Y, Xu Z, Xu G, Shen H. 16S rRNA gene sequencing analysis reveals an imbalance in the intestinal flora of Eriocheir sinensis with hepatopancreatic necrosis disease. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100988. [PMID: 35468457 DOI: 10.1016/j.cbd.2022.100988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Hepatopancreas necrosis disease (HPND) is a highly fatal disease that first appeared in Jiangsu Province, China, in 2015, and later spread to many other provinces, which had a severe impact on the culture of Chinese mitten crab (Eriocheir sinensis). Here, changes in the intestinal flora of healthy and HPND-affected Chinese mitten crabs were compared via 16S rRNA sequencing. Our findings indicated that Firmicutes, Bacteroidota, and Proteobacteria were the three dominant phyla in both healthy and HPND-affected crabs and exhibited no significant differences in α-diversity (richness p = 0.0892; evenness and diversity p = 0.0630). Furthermore, there were no significant changes in the abundance of Proteobacteria between the experimental groups. However, the abundance of Bacteroidota in the HPND group was significantly higher than that of the control group (HPND: 30.12%, Control: 16.60%), whereas the abundance of Firmicutes was significantly lower (HPND: 29.90%, Control: 50.55%). At the genus level, the abundance of Candidatus Bacilloplasma, Desulfovibrio, Bacteroides, and Aeromonas also differed significantly between groups (P < 0.05). Collectively, our study confirms an imbalance in the gut microbiota of Chinese mitten crabs with HPND and we speculate that this alteration may affect the metabolism and immune function of these organisms. Furthermore, we suspect that the structural changes in the intestinal flora of sick crabs observed in our study may be related to HPND.
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Affiliation(s)
- Ming Zhan
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Changjun Xi
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jie Gong
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Mengru Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Yan Shui
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Zenghong Xu
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Gangchun Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Huaishun Shen
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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12
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Zhou K, Qin Y, Song Y, Zhao K, Pan W, Nan X, Wang Y, Wang Q, Li W. A Novel Ig Domain-Containing C-Type Lectin Triggers the Intestine-Hemocyte Axis to Regulate Antibacterial Immunity in Crab. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2343-2362. [PMID: 35508356 DOI: 10.4049/jimmunol.2101027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/06/2022] [Indexed: 12/22/2022]
Abstract
The C-type lectin family with the signature C-type lectin-like domain promotes antibacterial host defense within the animal kingdom. We examined the role of Chinese mitten crab, Eriocheir sinensis (H. Milne-Edwards) (Decapoda: Grapsidae) Ig domain-containing C-type lectin (EsIgLectin), a novel and poorly understood member of the C-type lectin family. EsIgLectin was expressed primarily by both hemocytes (E sinensis) and intestines, with significantly induced mRNA expression on intestinal or hemolymph bacterial infections. As a soluble protein, both its C-type lectin-like domain and the Ig domain were required for bacterial binding, bacterial agglutination, bacterial growth inhibition, and in vivo bacterial clearance. Polymeric EsIgLectin could be constructed via the disulfide bond in the Ig domain, significantly enhancing EsIgLectin antibacterial activity. EsIgLectin promoted bacterial phagocytosis in an Ig domain-dependent manner in hemocytes, while it controlled microbial homeostasis and protected against bacteria-induced inflammation in the intestine. Protein interaction studies revealed that the EsIgLectin Ig domain bound to the first Ig domain of the polymeric Ig receptor, which was essential for EsIgLectin-induced bacterial phagocytosis. The temporal sequence of cell interactions during intestinal inflammation is only beginning to be understood. In this article, we show that hemocyte-derived EsIgLectin entered the intestinal wall at the later phase of intestinal inflammation. Moreover, EsIgLectin protected the host against intestinal and hemolymph infections in a polymeric Ig receptor-dependent manner. Therefore, the EsIgLectin promoted bacterial clearance and protected against inflammatory disease through an independent or synergistic effect of hemocytes and intestines in invertebrates.
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Affiliation(s)
- Kaimin Zhou
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Yukai Qin
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Yu Song
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Ke Zhao
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Weijuan Pan
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Xingyu Nan
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Yue Wang
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Qun Wang
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Weiwei Li
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
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13
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Lailaja VP, Sumithra TG, Reshma KJ, Anusree VN, Amala PV, Kishor TG, Sanil NK. Characterization of novel L-asparaginases having clinically safe profiles from bacteria inhabiting the hemolymph of the crab, Scylla serrata (Forskål, 1775). Folia Microbiol (Praha) 2022; 67:491-505. [PMID: 35138564 DOI: 10.1007/s12223-022-00952-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/24/2022] [Indexed: 11/04/2022]
Abstract
L-asparaginase (ASNase) is the principal chemotherapeutic agent against different blood cancers. The risks associated with current clinical preparations demand screening for novel ASNases. Accordingly, the study was conducted to shortlist ASNases having clinically safer profiles from a novel niche, namely, microbes in the gut and hemolymph of apparently healthy Scylla serrata. A four-step strategic approach incorporating the essential requirements for clinically safer profiles was followed. The initial step through plate assay showed five (9.61%) potential ASNase producers. The relative prevalence of ASNase producers was higher in hemolymph (13.33%) than gut (4.5%). The positive isolates were identified as Priestia aryabhattai, Priestia megaterium, Bacillus altitudinis, Shewanella decolorationis, and Chryseomicrobium amylolyticum. Quantitative profiles revealed high ASNase production (114.29 to 287.36 U/mL) without any optimization, with an added advantage of the extracellular production. The second step for substrate specificity studies revealed the absence of L-glutaminase and urease activities in ASNases from C. amylolyticum and P. megaterium, the most desirable properties for safe clinical applications. This is the first report of glutaminase and urease-free ASNase from these two bacteria. The third step ensured type II nature of selected ASNases, the targeted form in clinical applications. The fourth step confirmed the activity and stability in human physiological conditions. Altogether, the results revealed two potential ASNases with clinically compatible profiles.
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Affiliation(s)
- V P Lailaja
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
| | - T G Sumithra
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India.
| | - K J Reshma
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
| | - V N Anusree
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
| | - P V Amala
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
| | - T G Kishor
- Fishery Resources Assessment Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
| | - N K Sanil
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
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14
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Wale M, Daffonchio D, Fusi M, Marasco R, Garuglieri E, Diele K. The Importance of Larval Stages for Considering Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization. Front Microbiol 2021; 12:770245. [PMID: 34721372 PMCID: PMC8555880 DOI: 10.3389/fmicb.2021.770245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Matthew Wale
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Daniele Daffonchio
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marco Fusi
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Ramona Marasco
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Elisa Garuglieri
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Karen Diele
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
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15
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Guan W, Li K, Zhao S, Li K. A high abundance of Firmicutes in the intestine of chinese mitten crabs (Eriocheir sinensis) cultured in an alkaline region. AMB Express 2021; 11:141. [PMID: 34693464 PMCID: PMC8542526 DOI: 10.1186/s13568-021-01301-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/12/2021] [Indexed: 12/31/2022] Open
Abstract
The Chinese mitten crab (Eriocheir sinensis) is a popular aquaculture product in East Asia, especially in China. In the last decade, rice-crab co-culture has rapidly expanded in China. Under this model, crabs are raised in rice fields instead of in traditional aquaculture ponds. In this study, we cultured two varieties of Chinese mitten crabs (Changjiang and Liaohe) in an alkaline region in northwest China and used Illumina MiSeq sequencing to compare the intestinal bacterial alpha diversity and community structure between traditional and co-culture aquaculture models, between two crab varieties, and between female and male crabs. Significant variations in intestinal bacterial communities were found between crab varieties and between female and male crabs but not between aquaculture models. These results show that rice-crab co-culture operations did not obviously impact the crab intestinal bacterial community compared with traditional pond aquaculture. Firmicutes was the most abundant bacterial phylum in the crab intestines (78%, relative abundance). Three dominant operational taxonomic units (OTUs) represented 73.2% of Firmicutes sequences and 56.8% of all sequences. A dominant OTU assigned as Firmicutes that was negatively correlated with crab body length, width, and weight was found in the source water for the experimental area. The results of this study suggest that the aquaculture of Chinese mitten crabs in alkaline regions requires more study to improve cultivation techniques.
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16
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Lin W, Lu J, Yao H, Lu Z, He Y, Mu C, Wang C, Shi C, Ye Y. Elevated pCO 2 alters the interaction patterns and functional potentials of rearing seawater microbiota. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 287:117615. [PMID: 34171732 DOI: 10.1016/j.envpol.2021.117615] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Mean oceanic CO2 values have already risen and are expected to rise further on a global scale. Elevated pCO2 (eCO2) changes the bacterial community in seawater. However, the ecological association of seawater microbiota and related geochemical functions are largely unknown. We provide the first evidence that eCO2 alters the interaction patterns and functional potentials of microbiota in rearing seawater of the swimming crab, Portunus trituberculatus. Network analysis showed that eCO2 induced a simpler and more modular bacterial network in rearing seawater, with increased negative associations and distinct keystone taxa. Using the quantitative microbial element cycling method, nitrogen (N) and phosphorus (P) cycling genes exhibited the highest increase after one week of eCO2 stress and were significantly associated with keystone taxa. However, the functional potential of seawater bacteria was decoupled from their taxonomic composition and strongly coupled with eCO2 levels. The changed functional potential of seawater bacteria contributed to seawater N and P chemistry, which was highlighted by markedly decreased NH3, NH4+-N, and PO43--P levels and increased NO2--N and NO3--N levels. This study suggests that eCO2 alters the interaction patterns and functional potentials of seawater microbiota, which lead to the changes of seawater chemical parameters. Our findings provide new insights into the mechanisms underlying the effects of eCO2 on marine animals from the microbial ecological perspective.
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Affiliation(s)
- Weichuan Lin
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo, China
| | - Jiaqi Lu
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo, China
| | - Huaiying Yao
- Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo, China
| | - Zhibin Lu
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China
| | - Yimin He
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo, China
| | - Changkao Mu
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo, China
| | - Chunlin Wang
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo, China
| | - Ce Shi
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo, China
| | - Yangfang Ye
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo, China.
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17
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Sepúlveda-Correa A, Daza-Giraldo LV, Polanía J, Arenas NE, Muñoz-García A, Sandoval-Figueredo AV, Vanegas J. Genes associated with antibiotic tolerance and synthesis of antimicrobial compounds in a mangrove with contrasting salinities. MARINE POLLUTION BULLETIN 2021; 171:112740. [PMID: 34304060 DOI: 10.1016/j.marpolbul.2021.112740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/22/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Salinity and wastewater pollution in mangrove ecosystems can affect microorganisms and the abundance of genes involved in response to these stressors. This research aimed to identify genes associated with resistance and biosynthesis of antimicrobial compounds in mangrove soils subjected to contrasting salinities and wastewater pollution. Samples of rhizospheric soil were taken from a mangrove at the mouth of the Ranchería River in La Guajira, Colombia. A functional analysis was performed using Illumina HiSeq 2500 sequencing data obtained from total DNA extracted. Increased salt concentration influenced metabolic pathways and differential abundance of genes associated with the synthesis of antimicrobial compounds (e.g., rfbB/rffG, INO1/ISYNA1, rfbA/rffH, sat/met3, asd). Also, among 33 genes involved in intrinsic antibiotic resistance, 16 were significantly influenced by salinity (e.g., cusR/copR/silR, vgb, tolC). We concluded that salt stress tolerance and adaptive mechanisms could favor the biosynthesis of antimicrobial compounds in mangroves contaminated by sewage.
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Affiliation(s)
| | | | - Jaime Polanía
- Universidad Nacional de Colombia Sede Medellín, Cra. 65 #59a-110, Medellín, Colombia
| | - Nelson E Arenas
- Universidad Antonio Nariño, Sede Circunvalar, Cra 3 Este No. 47 A 15, Bogotá, Colombia
| | | | | | - Javier Vanegas
- Universidad Antonio Nariño, Sede Circunvalar, Cra 3 Este No. 47 A 15, Bogotá, Colombia.
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18
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Béziat NS, Duperron S, Halary S, Azede C, Gros O. Bacterial ectosymbionts colonizing gills of two Caribbean mangrove crabs. Symbiosis 2021. [DOI: 10.1007/s13199-021-00801-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Redfern LK, Jayasundara N, Singleton DR, Di Giulio RT, Carlson J, Sumner SJ, Gunsch CK. The role of gut microbial community and metabolomic shifts in adaptive resistance of Atlantic killifish (Fundulus heteroclitus) to polycyclic aromatic hydrocarbons. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 776:145955. [PMID: 33647645 PMCID: PMC8294123 DOI: 10.1016/j.scitotenv.2021.145955] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 05/14/2023]
Abstract
Altered gut microbiomes may play a role in rapid evolution to anthropogenic change but remain poorly understood. Atlantic killifish (Fundulus heteroclitus) in the Elizabeth River, VA have evolved resistance to polycyclic aromatic hydrocarbons (PAHs) and provide a unique opportunity to examine the links between shifts in the commensal microbiome and organismal physiology associated with evolved resistance. Here, 16S rRNA sequence libraries derived from fish guts and sediments sampled from a highly PAH contaminated site revealed significant differences collected at similar samples from an uncontaminated site. Phylogenetic groups enriched in the libraries derived from PAH-resistant fish were dissimilar to their associated sediment libraries, suggesting the specific environment within the PAH-resistant fish intestine influence the gut microbiome composition. Gut metabolite analysis revealed shifts between PAH-resistant and non-resistant subpopulations. Notably, PAH-resistant fish exhibited reduced levels of tryptophan and increased levels of sphingolipids. Exposure to PAHs appears to impact several bacterial in the gut microbiome, particularly sphingolipid containing bacteria. Bacterial phylotypes known to include species containing sphingolipids were generally lower in the intestines of fish subpopulations exposed to high concentrations of PAHs, inferring a complex host-microbiome relationship. Overall, killifish microbial community shifts appear to be related to a suppression of overall metabolite level, indicating a potential role of the gut in organismal response to anthropogenic environmental change. These results on microbial and metabolomics shifts are potentially linked to altered bioenergetic phenotype observed in the same PAH-resistant killifish populations in other studies.
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Affiliation(s)
- Lauren K Redfern
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC 27713, United States of America; Department of Environmental and Civil Engineering, Florida Gulf Coast University, Fort Myers, FL 33965, United States of America
| | - Nishad Jayasundara
- Nicholas School of the Environment, Duke University, Durham, NC 27713, United States of America
| | - David R Singleton
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC 27713, United States of America
| | - Richard T Di Giulio
- Nicholas School of the Environment, Duke University, Durham, NC 27713, United States of America
| | - James Carlson
- Alternative BioMedical Solutions, Carrollton, TX 75006, United States of America
| | - Susan J Sumner
- Nutrition Research Institute, University of North Carolina, Chapel Hill, NC 27599, United States of America
| | - Claudia K Gunsch
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC 27713, United States of America.
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20
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Shen Z, Kumar D, Liu X, Yan B, Fang P, Gu Y, Li M, Xie M, Yuan R, Feng Y, Hu X, Cao G, Xue R, Chen H, Liu X, Gong C. Metatranscriptomic Analysis Reveals an Imbalance of Hepatopancreatic Flora of Chinese Mitten Crab Eriocheir sinensis with Hepatopancreatic Necrosis Disease. BIOLOGY 2021; 10:biology10060462. [PMID: 34071147 PMCID: PMC8224665 DOI: 10.3390/biology10060462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 01/05/2023]
Abstract
Simple Summary The cause of Chinese mitten crab Eriocheir sinensis hepatopancreas necrosis disease (HPND) remains a mystery. In this study, metatranscriptomics sequencing was conducted to characterize the changes in the structure and gene expression of hepatopancreatic flora of crabs with and without typical symptoms of HPND; an imbalance of hepatopancreatic flora can be found in the crab with HPND, and the detected microbial taxa decreased, whereas the prevalence of Spiroplasma eriocheiris significantly increased in the hepatopancreatic flora of crabs with typical symptoms of HPND, and the relative abundances of the virus and microsporidia in crabs with HPND were very low and did not increase with disease progression. The differentially-expressed genes (DEGs) in hepatopancreatic flora between crabs with and without HPND were enriched ribosome, retinol metabolism, and biosynthesis of unsaturated fatty acid KEGG pathways. These results suggested that an imbalance of hepatopancreatic flora was associated with crab HPND, and the enriched pathways of DEGs were associated with the pathological mechanism of HPND. Abstract Hepatopancreas necrosis disease (HPND) of the Chinese mitten crab Eriocheir sinensis causes huge economic loss in China. However, the pathogenic factors and pathogenesis are still a matter of dissension. To search for potential pathogens, the hepatopancreatic flora of diseased crabs with mild symptoms, diseased crabs with severe symptoms, and crabs without visible symptoms were investigated using metatranscriptomics sequencing. The prevalence of Absidia glauca and Candidatus Synechococcus spongiarum decreased, whereas the prevalence of Spiroplasma eriocheiris increased in the hepatopancreatic flora of crabs with HPND. Homologous sequences of 34 viral species and 4 Microsporidian species were found in the crab hepatopancreas without any significant differences between crabs with and without HPND. Moreover, DEGs in the hepatopancreatic flora between crabs with severe symptoms and without visible symptoms were enriched in the ribosome, retinol metabolism, metabolism of xenobiotics by cytochrome P450, drug metabolism—cytochrome P450, biosynthesis of unsaturated fatty acids, and other glycan degradation. Moreover, the relative abundance of functions of DEDs in the hepatopancreatic flora changed with the pathogenesis process. These results suggested that imbalance of hepatopancreatic flora was associated with crab HPND. The identified DEGs were perhaps involved in the pathological mechanism of HPND; nonetheless, HPND did not occur due to virus or microsporidia infection.
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Affiliation(s)
- Zeen Shen
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Dhiraj Kumar
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
- School of Studies in Zoology, Jiwaji University, Gwalior 474011, India
| | - Xunmeng Liu
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Disease, Nanjing 210036, China; (X.L.); (P.F.); (R.Y.); (H.C.); (X.L.)
| | - Bingyu Yan
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Ping Fang
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Disease, Nanjing 210036, China; (X.L.); (P.F.); (R.Y.); (H.C.); (X.L.)
| | - Yuchao Gu
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Manyun Li
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Meiping Xie
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Rui Yuan
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Disease, Nanjing 210036, China; (X.L.); (P.F.); (R.Y.); (H.C.); (X.L.)
| | - Yongjie Feng
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Xiaolong Hu
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
- Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou 215123, China
| | - Guangli Cao
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
- Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou 215123, China
| | - Renyu Xue
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
- Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou 215123, China
| | - Hui Chen
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Disease, Nanjing 210036, China; (X.L.); (P.F.); (R.Y.); (H.C.); (X.L.)
| | - Xiaohan Liu
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Disease, Nanjing 210036, China; (X.L.); (P.F.); (R.Y.); (H.C.); (X.L.)
| | - Chengliang Gong
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
- Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou 215123, China
- Correspondence:
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Apine E, Rai P, Mani MK, Subramanian V, Karunasagar I, Godhe A, Turner LM. Comparative analysis of the intestinal bacterial communities in mud crab Scylla serrata in South India. Microbiologyopen 2021; 10:e1179. [PMID: 33970543 PMCID: PMC8088116 DOI: 10.1002/mbo3.1179] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
Little is known about the functions of the crustacean gut microbiome, but environmental parameters and habitat are known to affect the composition of the intestinal microbiome, which may in turn affect the physiological status of the host. The mud crab Scylla serrata is an economically important species, and is wild‐caught, and farmed across the Indo‐Pacific region. In this study, we compared the composition of the gut microbiome (in terms of gut microbial species richness and abundance) of S. serrata collected from wild sites, and farms, from the east and west coast of India, and also tested the effects of the environment on the composition. The water temperature had a statistically significant effect on gut microbiome composition, with microbial biodiversity decreasing with increasing water temperature. This could have negative effects on both wild and farmed mud crabs under future climate change conditions, although further research into the effects of temperature on gut microbiomes is required. By comparison, salinity, crab mass and carapace width, geographical location as well as whether they were farmed or wild‐caught crabs did not have a significant impact on gut microbiome composition. The results indicate that farming does not significantly alter the composition of the gut microbiome when compared to wild‐caught crabs.
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Affiliation(s)
- Elina Apine
- Marine Biology and Ecology Research Centre, University of Plymouth, Plymouth, UK
| | - Praveen Rai
- Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangaluru, India
| | - Madhu K Mani
- Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangaluru, India
| | | | - Indrani Karunasagar
- Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangaluru, India
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Lucy M Turner
- Marine Biology and Ecology Research Centre, University of Plymouth, Plymouth, UK
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22
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Presence and activity of endo-β-1,4-mannase, an important digestive carbohydrase within the digestive fluid of terrestrial crustaceans. J Comp Physiol B 2021; 191:243-253. [PMID: 33544166 DOI: 10.1007/s00360-021-01342-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/04/2021] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
Within the midgut gland of the Christmas Island red crab, Gecarcoidea natalis, a single transcript for a GH5_10 endo-β-1,4-mannase had the highest expression out of all of the carbohydrase enzymes (Gan et al. in Mar Biotechnol 20:654-665, 2018). The activity, and potential digestive importance of this hemicellulase, compared with other carbohydrases, has yet to be established. The digestive fluid of G. natalis contained substantial endo-β-1,4-mannase activities (630 ± 55 (6) nmol reducing sugars. min-1. mg-1 protein). It was present as a single isozyme of 66.3 ± 0.7 kDa (n = 6). Endo-β-1,4-mannase activities were higher than that for lichenase and endo-β-1,4-glucanase but lower than that for β-1,3-glucanase and amylase. The digestive fluid was able to hydrolyse, galactomannan, into its component monosaccharides. Hence, this confirms expression data that this enzyme is one of the most important digestive cellulases/ hemicellulases. Expression of GH5_10 endo-β-1,4-mannase mRNA was consistent with that of a digestive enzyme, as it was expressed in the digestive midgut gland but not in muscle and gill. Endo-β-1,4-mannase activities were also present within the digestive fluid of the terrestrial hermit crabs, Coenobita perlatus and Coenobita brevimanus. Endo-β-1,4-mannase activities (1351 ± 136 (n=3) nmol reducing sugars. min-1 mg-1 protein for C. perlatus. 665 ± 32 n=(5) nmol reducing sugars. min-1 mg-1 protein for C. brevimanus) were higher than that for endo-β-1,4-glucanase and amylase but were lower than β-1,3-glucanase activities. Animals within the terrestrial hermit crab family, Coenobitidae consume legume and palm seeds which contain substantial amounts of mannan. Hence, high endo-β-1,4-mannase activities suggest that digestion of mannan within these species may represent an important source of carbohydrate.
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23
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Li W, Lu H, He Z, Sang Y, Sun J. Quality characteristics and bacterial community of a Chinese salt-fermented shrimp paste. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Brown BRP, Nunez JCB, Rand DM. Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides. Anim Microbiome 2020; 2:41. [PMID: 33499976 PMCID: PMC7807441 DOI: 10.1186/s42523-020-00058-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/16/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Natural populations inhabiting the rocky intertidal experience multiple ecological stressors and provide an opportunity to investigate how environmental differences influence microbiomes over small geographical scales. However, very few microbiome studies focus on animals that inhabit the intertidal. In this study, we investigate the microbiome of the intertidal barnacle Semibalanus balanoides. We first describe the microbiome of two body tissues: the feeding appendages, or cirri, and the gut. Next, we examine whether there are differences between the microbiome of each body tissue of barnacles collected from the thermally extreme microhabitats of the rocky shores' upper and lower tidal zones. RESULTS Overall, the microbiome of S. balanoides consisted of 18 phyla from 408 genera. Our results showed that although cirri and gut microbiomes shared a portion of their amplicon sequence variants (ASVs), the microbiome of each body tissue was distinct. Over 80% of the ASVs found in the cirri were also found in the gut, and 44% of the ASVs found in the gut were also found in the cirri. Notably, the gut microbiome was not a subset of the cirri microbiome. Additionally, we identified that the cirri microbiome was responsive to microhabitat differences. CONCLUSION Results from this study indicate that S. balanoides maintains distinct microbiomes in its cirri and gut tissues, and that the gut microbiome is more stable than the cirri microbiome between the extremes of the intertidal.
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Affiliation(s)
- Bianca R P Brown
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI, 02912, USA.
- Institute at Brown for Environment and Society, Brown University, 85 Waterman St., Providence, RI, 02912, USA.
| | - Joaquin C B Nunez
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI, 02912, USA
- Department of Biology, University of Virginia, 485 McCormick Road, Charlottesville, VA, 22904, USA
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI, 02912, USA.
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25
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Su S, Munganga BP, Du F, Yu J, Li J, Yu F, Wang M, He X, Li X, Bouzoualegh R, Xu P, Tang Y. Relationship Between the Fatty Acid Profiles and Gut Bacterial Communities of the Chinese Mitten Crab ( Eriocheir sinensis) From Ecologically Different Habitats. Front Microbiol 2020; 11:565267. [PMID: 33178151 PMCID: PMC7593381 DOI: 10.3389/fmicb.2020.565267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota plays an important role in a variety of physiological functions such as intestinal digestion, metabolic homeostasis, immune response, and responses to disease treatment. Whether there is a relationship between gut microbial communities and fatty acid (FA) profiles of Chinese mitten crab is unclear. Hence, we analyzed the relationship between FA profiles and the gut bacterial communities of six Chinese mitten crab (Eriocheir sinensis) populations from different lakes. The crabs were sampled from six different lakes in Jiangsu Province, China. The FA profiles of these crab populations were compared and clustered, and then used to determine the relationship between geographic location and FA composition. We also characterized the gut microbial communities of these crabs using 16S rRNA high-throughput gene sequencing. The FA profiles varied significantly (P < 0.05) between crabs from different geographical locations. A similar trend was also observed in the gut microbial communities, which also varied significantly based on their geographical origin (P < 0.05). Furthermore, alpha diversity, cluster analysis, and matching bacterial community structures with specific locations revealed patterns that significantly linked FA profiles to the gut microbiota. Further analysis of FA profiles and gut microbial community generated patterns that linked the two parameters. Hence, it was observed that the gut microbial community seems to contribute significantly to the FA composition of the Chinese mitten crab. However, further studies need to be conducted to investigate the interactions between gut microbial communities and the biochemical composition of the Chinese mitten crab, which will ultimately unravel the complexity of microbial ecosystems for potential applications in aquaculture and species conservation.
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Affiliation(s)
- Shengyan Su
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | | | - Fukuan Du
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Juhua Yu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jianlin Li
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Fan Yu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Meiyao Wang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinjin He
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinyuan Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Raouf Bouzoualegh
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Pao Xu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Yongkai Tang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
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Lin S, Kong T, Ren X, Li S, Gong Y. Elucidation of Gut Microbiota in Mud Crab Scylla paramamosain Challenged to WSSV and Aeromonas hydrophila. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:661-672. [PMID: 32914203 DOI: 10.1007/s10126-020-09987-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Mud crab Scylla paramamosain (S. paramamosain) is an economically important marine crab species around the world. White spot syndrome virus (WSSV) and Aeromonas hydrophila (AH) are pathogens during mud crab mariculture. It has been reported that gut microbiota possessed a great impact on the host development, nutrition, immunity, and disease resistance. However, little information was known about the impacts of WSSV or AH infection on the structure, composition, and function of the gut microbiotain of mud crabs. In this study, the gut microbiota of mud crabs infected with A. hydrophila and WSSV were characterized. The results showed that the composition and bacteria correlation of the gut microbiota were significantly decreased. During A. hydrophila infection, the pathogens played a major regulatory role in host. While in the mud crabs infected with WSSV, many beneficial strains had a great impact on the host expect for the pathogens. Therefore, our study revealed the effect of pathogens infection on gut microbiota of mud crabs and clarified the difference between viral infection and bacterial infection.
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Affiliation(s)
- Shanmeng Lin
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Tongtong Kong
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Xin Ren
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Yi Gong
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China.
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China.
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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27
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Lv X, Li S, Yu Y, Zhang X, Li F. Characterization of a gill-abundant crustin with microbiota modulating function in Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2020; 105:393-404. [PMID: 32702477 DOI: 10.1016/j.fsi.2020.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/04/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Gills as the respiratory tissue of crustacean encounter various threats in the environment. The immune defense in gills is essential to the health of shrimp. In the present study, we identified a novel gill-abundant crustin, LvCrustin Ⅱ-1, from the shrimp Litopenaeus vannamei. The full-length open reading frame of LvCrustin Ⅱ-1 is 522 bp, which encodes 173 amino acid residues. The amino acid sequence of LvCrustin Ⅱ-1 contained a signal peptide, a glycine rich region, a cysteine rich region and a whey acidic protein (WAP) domain. The expression level of LvCrustin Ⅱ-1 was significantly up-regulated at different time points after Vibrio parahaemolyticus immersion. When LvCrustin Ⅱ-1 was silenced by dsRNA interference, the count of bacteria colonies increased significantly in the hepatopancreas of shrimp after V. parahaemolyticus immersion, which indicated that the infection progress of pathogenic bacteria was accelerated after LvCrustin Ⅱ-1 knockdown. Compared with the microbiota of seawater, the lower proportion of aquatic bacteria and higher proportion of symbiont in the gills microbiota of shrimp indicated the bacterial colonization was modulated by the host. Knockdown of LvCrustin Ⅱ-1 changed the proportion of some potential pathogens and aquatic bacteria, which supported the idea that the new identified crustin in the gills played important roles in modulation of the microbiota community in shrimp. The present data provided new insights into the multiple functions of crustin in the immunity of shrimp.
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Affiliation(s)
- Xinjia Lv
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, China.
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28
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Hong Y, Huang Y, Wu S, Yang X, Dong Y, Xu D, Huang Z. Effects of imidacloprid on the oxidative stress, detoxification and gut microbiota of Chinese mitten crab, Eriocheir sinensis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:138276. [PMID: 32361427 DOI: 10.1016/j.scitotenv.2020.138276] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Imidacloprid (IMI) is used in integrated aquaculture systems for pest control and the toxicity of IMI to non-target aquatic animals such as fish and microcrustaceans has been recognised. However, knowledge about the toxic effect of IMI on commercial crabs is still scarce. In the present study, effects of IMI on the acute toxicity, antioxidative status, detoxification systems and gut microbiota in Chinese mitten crab, Erocheir sinensis were investigated. In the present study, the 96-h LC50 of IMI for E. sinensis was 24.97 mg/L. Under sublethal exposure, superoxide dismutase (SOD) activities increased under low concentration (LC, 5 μg/L) and median concentration (MC, 50 μg/L) exposure, but decreased in high concentration group (HC, 500 μg/L). Activities of catalyse (CAT) decreased in a dose-dependent manner. Detoxification-related enzymes aminopyrine N-demethylase (APND) and erythromycin N-demethylase (ERND) increased in all treatments whereas glutathione-S-transferase (GST) decreased dose-dependently. The relative mRNA expression of the cytochrome P4502 (cyp2) gene was induced significantly in LC and HC groups while no significant change was observed in cytochrome P4503 (cyp3) gene. The expression of gst was also significantly decreased in HC group. Up-regulation of heat shock protein hsp70 and 90 was observed in MC and HC groups whereas hsp60 up-regulated only in LC group. In addition, significant changes of composition of microbial communities at both phylum and genus levels were found in this test. In particular, beneficial bacteria were found to decrease and pathogens increased after exposure to IMI. These results indicate that high concentration of IMI could induce oxidative stress and suppress the detoxification system mainly by down-regulation of gst mRNA expression, inhibition of enzyme activities and dysbiosis of gut microbiota.
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Affiliation(s)
- Yuhang Hong
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang 415000, Sichuan Province, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture; Shanghai Engineering Research Centre of Agriculture, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New District, Shanghai 201306, China.
| | - Yi Huang
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang 415000, Sichuan Province, China
| | - Shu Wu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Road, Chengdu 611137, China
| | - Xiaozhen Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture; Shanghai Engineering Research Centre of Agriculture, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New District, Shanghai 201306, China
| | - Yanzhen Dong
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang 415000, Sichuan Province, China
| | - Dayong Xu
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang 415000, Sichuan Province, China
| | - Zhiqiu Huang
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang 415000, Sichuan Province, China
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Miao F, Zhao Z, Li Q, Song J, Wang Y, Hu M. Impact of Initial Feeding and Molting on Tachypleus tridentatus Gut Microbiota. Curr Microbiol 2020; 77:2847-2858. [PMID: 32617662 DOI: 10.1007/s00284-020-02108-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/23/2020] [Indexed: 11/26/2022]
Abstract
Tri-spine horseshoe crabs (HSCs) Tachypleus tridentatus have been facing the threat of population depletion for decades, and the physiology and microbiology of their early life stages are lacking. To explore what directs the change of juvenile T. tridentatus gut microbiota and how gut microbiota change, by using 16S rRNA sequencing of gut samples we detected the intestinal microbiome of juvenile HSCs and compared the impact of initial molting and initial feeding, as well as the effect of environment. Results showed that the predominant phyla in the gut microbial community of juvenile HSCs are Proteobacteria and Bacteroidetes. The richness and diversity of intestinal microbes greatly decreased after initial molting. Microbial-mediated functions predicted by PICRUSt showed that "Signal Transduction", "Cellular Processes and Signaling", "Infective Diseases" and "Digestive System" pathways significantly increased in 2nd instars. As for the effect of environment, the connection between living environment and the intestinal microbiome started to manifest after initial molting. Unexpectedly, initial feeding treatment slightly affected the intestinal microbiome of T. tridentatus in the early life stage, whereas the effect of initial molting was significant. The present study provided the first insight into the gut microbiota of T. tridentatus, and the findings led a new sight to explain what guide the change of gut microbiota.
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Affiliation(s)
- Fengze Miao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Zhonghao Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | | | - Jie Song
- Tianjin Era Biology Technology Co., Ltd., Tianjin, China
| | - Youji Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Menghong Hu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China.
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Detection of Extended-Spectrum β-Lactamases (ESBL) Producing Enterobacteriaceae from Fish Trapped in the Lagoon Area of Bizerte, Tunisia. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7132812. [PMID: 32596358 PMCID: PMC7303757 DOI: 10.1155/2020/7132812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 12/11/2022]
Abstract
Extended-spectrum β-lactamase and their molecular mechanism in Enterobacteriaceae were analyzed in 126 fish samples of 9 various wild species, living in the lagoon of Bizerte in Tunisia. Fifty-nine (59) Gram-negative strains were isolated and identified as Escherichia coli (n = 24), Klebsiella pneumonia (n = 21), Citrobacter freundii (n = 8), and Shigella boydii (n = 6). Forty-seven ESBL producers were identified using the synergic test. β-Lactamase genes detected were blaCTX-M-1 (E. coli/15; K. pneumonia/8; C. freundii/1; Sh. boydii/1), blaCTX-M-1+ blaOXA-1 (E. coli/4; K. pneumonia/3), blaCTX-M-1+ blaTEM-1-a (K. pneumonia/2), blaCTX-M-15+ blaTEM-1-a (K. pneumonia/1; Sh. boydii/1), blaCTX-M-15+ blaOXA-1 (K. pneumonia/1), blaCTX-M-15 (E. coli/3; K. pneumonia/1; Sh. boydii/3), and blaCTX-M-9 (C. freundii/3). Most strains (84.7%) showed a multiresistant phenotype. qnrA and qnrB genes were identified in six E. coli and in ten E. coli+one K. pneumonia isolates, respectively. The resistance to tetracycline and sulfonamide was conferred by the tet and sul genes. Characterization of phylogenic groups in E. coli isolates revealed phylogroups D (n = 20 strains), B2 (n = 2), and A (n = 2). The studied virulence factor showed prevalence of fimA genes in 9 E. coli isolates (37.5%). Similarly, no strain revealed the three other virulence factors tested (eae, aer, and cnf1). Our findings confirmed that the lagoons of Bizerte may be a reservoir of multidrug resistance/ESBL-producing Enterobacteriaceae. This could lead to indisputable impacts on human and animal health, through the food chain.
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Dai W, Xiong J, Zheng H, Ni S, Ye Y, Wang C. Effect of Rhizophora apiculata plantation for improving water quality, growth, and health of mud crab. Appl Microbiol Biotechnol 2020; 104:6813-6824. [PMID: 32514755 DOI: 10.1007/s00253-020-10716-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/21/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023]
Abstract
A deteriorated water quality is closely associated with disease outbreaks in aquaculture, where microorganisms play indispensable roles in improving water quality and aquatic animals' health. Mangrove is known to be a natural water quality filter and microbiological buffer of pathogen and prebiotics. However, it is unclear how and to what extent Rhizophora apiculata plantation is of benefits to the gut microbiota and growth over mud crab (Scylla paramamosain) aging. To address these concerns, we explored the bacterial communities in mud crab gut and rearing water at 45, 114, and 132 days after incubation, roughly corresponding to juvenile, pre-adult, and adult stages of mud crab. Results showed that 1-year R. apiculata plantation slightly increased the body weight of mud crab and improved water quality to a certain extent. Both bacterioplankton and gut bacterial communities were highly temporal dynamic, while the two communities were significantly distinct (ANOSIM r = 0.90, P = 0.0001). Relative abundances of dominant taxa in water and gut significantly varied between the plantation and the control conditions over mud crab aging. R. apiculata plantation promoted the stability of gut microbiota, as evidenced by more diverse core species. Furthermore, R. apiculata plantation led to the dominance of Verrucomicrobiae species in water and probiotic Bacteroidetes and Lactobacillales taxa in gut. A structural equation model revealed that water variables directly constrained gut microbiota, which in turn affected the body weight of mud crab (r = 0.52, P < 0.001). In addition, functional pathways facilitating immunity and lipid metabolism significantly increased in mud crab gut under the plantation, while those involved in infectious diseases exhibited the opposing trend. These findings greatly expand our understanding of the R. apiculata plantation effects on water quality, gut microbiota, and growth feature of mud crab. Overall, R. apiculata plantation is beneficial for mud crab growth and health. KEY POINTS: • A short-term R. apiculata plantation could potentially improve water quality. • Bacterioplankton is more sensitive than mud crab gut microbiota in response to R. apiculata plantation. • R. apiculata plantation enhances mud crab resistance against pathogen invasion. • R. apiculata plantation alters mud crab gut microbiota, which in turn promotes their body weight.
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Affiliation(s)
- Wenfang Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China. .,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.
| | - Hao Zheng
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Sui Ni
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Yangfang Ye
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Chunlin Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China. .,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
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Holt CC, Bass D, Stentiford GD, van der Giezen M. Understanding the role of the shrimp gut microbiome in health and disease. J Invertebr Pathol 2020; 186:107387. [PMID: 32330478 DOI: 10.1016/j.jip.2020.107387] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/05/2020] [Accepted: 04/17/2020] [Indexed: 02/08/2023]
Abstract
With rapid increases in the global shrimp aquaculture sector, a focus on animal health during production becomes ever more important. Animal productivity is intimately linked to health, and the gut microbiome is becoming increasingly recognised as an important driver of cultivation success. The microbes that colonise the gut, commonly referred to as the gut microbiota or the gut microbiome, interact with their host and contribute to a number of key host processes, including digestion and immunity. Gut microbiome manipulation therefore represents an attractive proposition for aquaculture and has been suggested as a possible alternative to the use of broad-spectrum antibiotics in the management of disease, which is a major limitation of growth in this sector. Microbiota supplementation has also demonstrated positive effects on growth and survival of several different commercial species, including shrimp. Development of appropriate gut supplements, however, requires prior knowledge of the host microbiome. Little is known about the gut microbiota of the aquatic invertebrates, but penaeid shrimp are perhaps more studied than most. Here, we review current knowledge of information reported on the shrimp gut microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of Proteobacteria within this community. We discuss involvement of the microbiome in the regulation of shrimp health and disease and describe how the gut microbiota changes with the introduction of several economically important shrimp pathogens. Finally, we explore evidence of microbiome supplementation and consider its role in the future of penaeid shrimp production.
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Affiliation(s)
- Corey C Holt
- International Centre of Excellence for Aquatic Animal Health Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom; Biosciences, University of Exeter, Stocker Road, Exeter, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom; Department of Botany, University of British Columbia, Vancouver, Canada.
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom
| | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom
| | - Mark van der Giezen
- Biosciences, University of Exeter, Stocker Road, Exeter, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom; Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway.
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33
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Tang L, Wang H, Wang C, Mu C, Wei H, Yao H, Ye C, Chen L, Shi C. Temperature potentially induced distinctive flavor of mud crab Scylla paramamosain mediated by gut microbiota. Sci Rep 2020; 10:3720. [PMID: 32111891 PMCID: PMC7048764 DOI: 10.1038/s41598-020-60685-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/14/2020] [Indexed: 11/28/2022] Open
Abstract
Many factors affect the flavor of crabs. However, impact of temperature on flavor has not been reported. Here, we examined Scylla paramamosain collected within the main four producing areas in China from north sampling point (NP) and south sampling point (SP), respectively. The contents of flavouring-related substances in hepatopancreas, muscles and gonads were determined by high-performance liquid chromatography (HPLC). Meanwhile, high-throughput sequencing of 16S RNA gene was used to reveal the diversity distribution of gut microbiota at each sample collection point. Comparisons among flavor substances of edible parts, the implied higher temperature in SP may be beneficial to the accumulation of flavor substances in gonads, while lower temperature in NP may be beneficial to the accumulation of flavor substances in muscles and hepatopancreas. The gut microbiota of crabs, was analyzed via 16S rRNA gene sequencing. The results of gut microbiota showed that there were significant differences in the distribution of gut microbiota in NP and SP. The microbiota composition of SP has a high distribution richness and no absolute dominant bacteria, while NP has absolute dominant bacteria and its microbiota richness was lower than SP. The results of redundancy analysis (RDA) showed that there was a significant correlation between temperature and the relative abundance of gut microbiota, and a significant correlation between gut microbiota and the content of flavor substances. This study indicates that temperature may be one of the main factors for the differences of flavor substances between SP and NP, which was most probably mediated by gut microbiota. Further exploration is needed with laboratory experiments in which the environment is more precisely controlled if these views are to be determined.
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Affiliation(s)
- Lei Tang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Huan Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China. .,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Chunlin Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Changkao Mu
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Hongling Wei
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Hongzhi Yao
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Chunyu Ye
- Marine and Fishery Bureau, Sanmen County, Zhejiang Province, China.,Fishery Technology Station, Sanmen County, Zhejiang Province, China
| | - Lizhi Chen
- Marine and Fishery Bureau, Sanmen County, Zhejiang Province, China.,Fishery Technology Station, Sanmen County, Zhejiang Province, China
| | - Ce Shi
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China
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Holt CC, van der Giezen M, Daniels CL, Stentiford GD, Bass D. Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus). THE ISME JOURNAL 2020; 14:531-543. [PMID: 31676854 PMCID: PMC6976562 DOI: 10.1038/s41396-019-0546-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022]
Abstract
Microbial communities within the gut can markedly impact host health and fitness. To what extent environmental influences affect the differential distribution of these microbial populations may therefore significantly impact the successful farming of the host. Using a sea-based container culture (SBCC) system for the on-growing of European lobster (Homarus gammarus), we tracked the bacterial gut microbiota over a 1-year period. We compared these communities with lobsters of the same cohort, retained in a land-based culture (LBC) system to assess the effects of the culture environment on gut bacterial assemblage and describe the phylogenetic structure of the microbiota to compare deterministic and stochastic assembly across both environments. Bacterial gut communities from SBCCs were generally more phylogenetically clustered, and therefore deterministically assembled, compared to those reared in land-based systems. Lobsters in SBCCs displayed significantly more species-rich and species-diverse gut microbiota compared to those retained in LBC. A reduction in the bacterial diversity of the gut was also associated with higher infection prevalence of the enteric viral pathogen Homarus gammarus nudivirus (HgNV). SBCCs may therefore benefit the overall health of the host by promoting the assembly of a more diverse gut bacterial community and reducing the susceptibility to disease.
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Affiliation(s)
- Corey C Holt
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset, DT4 8UB, UK.
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
- The National Lobster Hatchery, South Quay, Padstow, UK.
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
| | - Mark van der Giezen
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
- Centre for Organelle Research, University of Stavanger, 4021, Stavanger, Norway
| | | | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset, DT4 8UB, UK
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset, DT4 8UB, UK.
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
- Department of Life Sciences, The Natural History Museum, Cromwell Road, Kensington, London, UK.
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35
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Deng Y, Cheng C, Feng J, Liu S, Ma H, Chen X, Chen H, Guo Z. Rapid environmental change shapes pond water microbial community structure and function, affecting mud crab (Scylla paramamosain) survivability. Appl Microbiol Biotechnol 2020; 104:2229-2241. [DOI: 10.1007/s00253-019-10328-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022]
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36
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The effect of dietary supplementation with Clostridium butyricum on the growth performance, immunity, intestinal microbiota and disease resistance of tilapia (Oreochromis niloticus). PLoS One 2019; 14:e0223428. [PMID: 31815958 PMCID: PMC6901227 DOI: 10.1371/journal.pone.0223428] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 09/20/2019] [Indexed: 12/31/2022] Open
Abstract
This study was conducted to assess the effects of dietary Clostridium butyricum on the growth, immunity, intestinal microbiota and disease resistance of tilapia (Oreochromis niloticus). Three hundreds of tilapia (56.21 ± 0.81 g) were divided into 5 groups and fed a diet supplemented with C. butyricum at 0, 1 x 104, 1 x 105, 1 x 106 or 1 x 107 CFU g-1 diet (denoted as CG, CB1, CB2, CB3 and CB4, respectively) for 56 days. Then 45 fish from each group were intraperitoneally injected with Streptococcus agalactiae, and the mortality was recorded for 14 days. The results showed that dietary C. butyricum significantly improved the specific growth rate (SGR) and feed intake in the CB2 group and decreased the cumulative mortality post-challenge with S. agalactiae in the CB2, CB3 and CB4 groups. The serum total antioxidant capacity and intestinal interleukin receptor-associated kinase-4 gene expression were significantly increased, and serum malondialdehyde content and diamine oxidase activity were significantly decreased in the CB1, CB2, CB3 and CB4 groups. Serum complement 3 and complement 4 concentrations and intestinal gene expression of tumour necrosis factor α, interleukin 8, and myeloid differentiation factor 88 were significantly higher in the CB2, CB3 and CB4 groups. Intestinal toll-like receptor 2 gene expression was significantly upregulated in the CB3 and CB4 groups. Dietary C. butyricum increased the diversity of the intestinal microbiota and the relative abundance of beneficial bacteria (such as Bacillus), and decreased the relative abundance of opportunistic pathogenic bacteria (such as Aeromonas) in the CB2 group. These results revealed that dietary C. butyricum at a suitable dose enhanced growth performance, elevated humoral and intestinal immunity, regulated the intestinal microbial components, and improved disease resistance in tilapia. The optimal dose was 1 x 105 CFU g-1 diet.
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37
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Wei H, Wang H, Tang L, Mu C, Ye C, Chen L, Wang C. High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China. BMC Genomics 2019; 20:829. [PMID: 31703624 PMCID: PMC6842235 DOI: 10.1186/s12864-019-6219-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 10/23/2019] [Indexed: 11/22/2022] Open
Abstract
Background Scylla paramamosain is a commercially important mud crab. The microbiota is a community that inhabits the crab intestine, and is important for physiological functional and host health. Results Proteobacteria, Firmicutes, Bacteroidetes, Tenericutes, Spirochaetae and Fusobacteria were the dominant phyla of the 36 representative phyla. Eleven genera of the 820 representative genera were considered as core gut microbiota and were distributed in the five dominant phyla. The core genus of the Proteobacteria included Arcobacter, Photobacterium, Vibrio, Shewanella and Desulfovibrio. The other four phyla contained one or two genera. Male and female crab samples had two different core genera, (male samples: Psychrilyobacter & Lactococcus; female samples: Clostridium_sensu_stricto_11 and Candidatus_Bacilloplasma). Conclusions This is the first time core intestinal microbiota have been identified in crab from nine coastal regions of southern China. This study provides sequencing data related to the gut microbiota of S. paramamosain, and may contribute to probiotic development for S. paramamosain aquaculture industries.
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Affiliation(s)
- Hongling Wei
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Huan Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China. .,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Lei Tang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Changkao Mu
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Chunyu Ye
- Agricultural and Rural Bureau, Sanmen County, Zhejiang Province, China
| | - Lizhi Chen
- Fishery Technology Station, Sanmen County, Zhejiang Province, China
| | - Chunlin Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China. .,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
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Cuellar-Gempeler C, Munguia P. Habitat filters mediate successional trajectories in bacterial communities associated with the striped shore crab. Oecologia 2019; 191:957-970. [PMID: 31690999 DOI: 10.1007/s00442-019-04549-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 10/28/2019] [Indexed: 02/01/2023]
Abstract
The relative importance of stochastic- and niche-based processes shifts during successional time and across different types of habitats. Microbial biofilms are known to undergo such successional shifts. However, little is known about the interaction between these successional trajectories and habitat filters. Harsh habitat filters could affect biofilm successional trajectories by strengthening niche-based processes and weakening stochastic processes. We used mesocosms to track successional trajectories in bacterial communities associated with the striped shore crab (Pachygrapsus transversus). We followed replicated microbial communities under strong and weak habitat filters associated with the crab's gut and carapace. For bacteria, colonization of the crab's gut is constrained by strong chemical and physical filtering, while the carapace remains relatively open for colonization. Consistent with successional models of bacterial biofilms, carapace microbial communities initially converged in community composition at day 8 and diverged thereafter. We expected gut microbial communities to deviate from the trajectory in the carapace and converge towards a subset of tolerant species. Instead, bacterial communities in the gut exhibited low richness, unchanging similarity in composition and turnover in species identities throughout the duration of our study. These habitat filter effects were linked with weak species interactions and low influence from colonization in the gut. If these findings are representative of differences in filter strength in a continuum of successional trajectories, habitat filters may provide basis for predictions that link successional models and habitat types.
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Affiliation(s)
| | - Pablo Munguia
- Royal Melbourne Institute of Technology, Melbourne, Australia
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39
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Dubé CE, Ky CL, Planes S. Microbiome of the Black-Lipped Pearl Oyster Pinctada margaritifera, a Multi-Tissue Description With Functional Profiling. Front Microbiol 2019; 10:1548. [PMID: 31333634 PMCID: PMC6624473 DOI: 10.3389/fmicb.2019.01548] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/20/2019] [Indexed: 12/21/2022] Open
Abstract
Elucidating the role of prokaryotic symbionts in mediating host physiology has emerged as an important area of research. Since oysters are the world’s most heavily cultivated bivalve molluscs, numerous studies have applied molecular techniques to understand the taxonomic and functional diversity of their associated bacteria. Here, we expand on this research by assessing the composition and putative functional profiles of prokaryotic communities from different organs/compartments of the black-lipped pearl oyster Pinctada margaritifera, a commercially important shellfish valued for cultured pearl production in the Pacific region. Seven tissues, in addition to mucous secretions, were targeted from P. margaritifera individuals: the gill, gonad, byssus gland, haemolymph, mantle, adductor muscle, mucus, and gut. Richness of bacterial Operational Taxonomic Units (OTUs) and phylogenetic diversity differed between host tissues, with mucous layers displaying the highest richness and diversity. This multi-tissues approach permitted the identification of consistent microbial members, together constituting the core microbiome of P. margaritifera, including Alpha- and Gammaproteobacteria, Flavobacteriia, and Spirochaetes. We also found a high representation of Endozoicimonaceae symbionts, indicating that they may be of particular importance to oyster health, survival and homeostasis, as in many other coral reef animals. Our study demonstrates that the microbial communities and their associated predicted functional profiles are tissue specific. Inferred physiological functions were supported by current physiological data available for the associated bacterial taxa specific to each tissue. This work provides the first baseline of microbial community composition in P. margaritifera, providing a solid foundation for future research into this commercially important species and emphasises the important effects of tissue differentiation in structuring the oyster microbiome.
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Affiliation(s)
- Caroline Eve Dubé
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France.,Laboratoire d'Excellence "CORAIL", Mo'orea, French Polynesia
| | - Chin-Long Ky
- Laboratoire d'Excellence "CORAIL", Mo'orea, French Polynesia.,Ifremer, UMR 241, Centre du Pacifique, Tahiti, French Polynesia.,Ifremer, UMR 5244 Interactions Hôtes Pathogènes Environnements, Université de Montpellier, Montpellier, France
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France.,Laboratoire d'Excellence "CORAIL", Mo'orea, French Polynesia
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40
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Li H, Mishra M, Ding S, Miyamoto MM. Diversity and Dynamics of "Candidatus Endobugula" and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina. MICROBIAL ECOLOGY 2019; 77:243-256. [PMID: 30141128 DOI: 10.1007/s00248-018-1233-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
Bugula neritina is a common invasive cosmopolitan bryozoan that harbors (like many sessile marine invertebrates) a symbiotic bacterial (SB) community. Among the SB of B. neritina, "Candidatus Endobugula sertula" continues to receive the greatest attention, because it is the source of bryostatins. The bryostatins are potent bioactive polyketides, which have been investigated for their therapeutic potential to treat various cancers, Alzheimer's disease, and AIDS. In this study, we compare the metagenomics sequences for the 16S ribosomal RNA gene of the SB communities from different geographic and life cycle samples of Chinese B. neritina. Using a variety of approaches for estimating alpha/beta diversity and taxonomic abundance, we find that the SB communities vary geographically with invertebrate and fish mariculture and with latitude and environmental temperature. During the B. neritina life cycle, we find that the diversity and taxonomic abundances of the SB communities change with the onset of host metamorphosis, filter feeding, colony formation, reproduction, and increased bryostatin production. "Ca. Endobugula sertula" is confirmed as the symbiont of the Chinese "Ca. Endobugula"/B. neritina symbiosis. Our study extends our knowledge about B. neritina symbiosis from the New to the Old World and offers new insights into the environmental and life cycle factors that can influence its SB communities, "Ca. Endobugula," and bryostatins more globally.
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Affiliation(s)
- Hai Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, China
| | - Mrinal Mishra
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611-8525, USA
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
| | - Michael M Miyamoto
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611-8525, USA
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41
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Dong J, Li X, Zhang R, Zhao Y, Wu G, Liu J, Zhu X, Li L. Comparative analysis of the intestinal bacterial community and expression of gut immunity genes in the Chinese Mitten Crab (Eriocheir sinensis). AMB Express 2018; 8:192. [PMID: 30547243 PMCID: PMC6292837 DOI: 10.1186/s13568-018-0722-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 02/07/2023] Open
Abstract
Remarkably little information is available about the interaction between the gut microbiota and intestinal immunity in fish and crustaceans. In our study, we used Illumina MiSeq sequencing and real-time quantitative PCR to compare the microbial community and immunity genes expression in the foregut, midgut and hindgut of Chinese mitten crab (Eriocheir sinensis). Our results indicated that the community richness of the midgut is higher than in the foregut or the hindgut, although the bacterial diversity in the hindgut is higher. The predominant phyla were Tenericutes and Firmicutes in the foregut, Tenericutes and Proteobacteria in the midgut and Proteobacteria, Tenericutes and Bacteroidetes in the hindgut. When compared with the midgut, the expression of antimicrobial peptides (AMPs) were significantly elevated in the hindgut (P < 0.05), and the gene expression of EsRelish (IMD pathway) was higher than the Toll signaling pathway genes. Actinobacteria and Lactobacillus had negative correlationship with the expression of AMPs, although Acinetobacter, Bacteroides, Flavobacterium can up-regulate the expression of AMP genes. Collectively, our data indicate that microbiota are site-specific within the digestive tracts of crabs and the bacterial community and intestinal immunity have a close relationship in E. sinensis.
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42
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Wang C, Zhou Y, Lv D, Ge Y, Li H, You Y. Change in the intestinal bacterial community structure associated with environmental microorganisms during the growth of Eriocheir sinensis. Microbiologyopen 2018; 8:e00727. [PMID: 30311433 PMCID: PMC6528601 DOI: 10.1002/mbo3.727] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/15/2022] Open
Abstract
As an important organ to maintain the host's homeostasis, intestinal microbes play an important role in development of the organism. In contrast to those of terrestrial animals, the intestinal microbes of aquatic organisms are affected by environmental microorganisms (including water microorganisms and sediment microorganisms). In the present study, the compositional differences of intestinal microbes in three representative developmental stages of the Chinese mitten crab (Eriocheir sinensis) were studied. Meanwhile, network association analysis, and visualization of the water microorganisms of the crabs’ habitat, the environment microorganisms in the pond, and the intestinal microbes, was carried out. The results showed that the gut microbiota diversity index decreased continuously with age, and the four bacteria of Aeromonas (Proteobacteria), Defluviitaleaceae (Firmicutes), Candidatus Bacilloplasma (Tenericutes), and Dysgonomonas (Bacteroidetes) were the “indigenous” flora of the crab. In the network‐related analysis with the environment, we found that as the culture time increased, the effect of environmental microorganisms on the intestinal microbes of crabs gradually decreased, and the four “indigenous” bacteria were always unaffected by the environmental microorganisms. The results of this study identified the core bacteria of the crab and, for the first time, studied the relationship between intestinal environmental microorganisms, which will aid the practical production of crabs and will promote research into the relationship between specific bacteria and the physiological metabolism of crabs.
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Affiliation(s)
- Chenhe Wang
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi, China
| | - Yanfeng Zhou
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture, Freshwater Fisheries Research Center, CAFS, WuXi, China
| | - Dawei Lv
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture, Freshwater Fisheries Research Center, CAFS, WuXi, China
| | - You Ge
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture, Freshwater Fisheries Research Center, CAFS, WuXi, China
| | - Huan Li
- Nextomics Biosciences Co., Ltd, Wuhan, China
| | - Yang You
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi, China.,Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture, Freshwater Fisheries Research Center, CAFS, WuXi, China
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43
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Rodrigues PA, Ferrari RG, Conte-Junior CA. Application of molecular tools to elucidate the microbiota of seafood. J Appl Microbiol 2018; 124:1347-1365. [PMID: 29345036 DOI: 10.1111/jam.13701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 12/19/2022]
Abstract
The aim of this review is to present the methodologies currently applied to identify microbiota and pathogens transmitted to humans through seafood consumption, focusing on molecular techniques and pointing out their importance, advantages, disadvantages and applicability. Knowledge of available techniques allows researchers to identify which technique best fits their expectations. With such discernment, it will be possible to infer which disadvantages will be present and, therefore, not interfering with the final result. Two methodologies can be employed for this purpose, dependent and independent cultures. However, the dependent culture has certain limitations that can be solved through the independent cultivation techniques, such as PCR, PFGE and NGS, especially through the sequencing of the 16S rRNA region, providing a complete view of microbial diversity. These have revolutionized microbiological knowledge, mainly because they allow for the identification of uncultivable micro-organisms, which represent a substantial portion of total micro-organisms, making it possible to elucidate not yet described taxa which may display pathogenic potential, besides quantifying microbial communities, microbiota genetics, translated proteins and produced metabolites. In addition, transcriptomic and metabolomic techniques also allow for the evaluation of possible impacts that microbial communities may create in their environment, as well as the determination of potential pathogenicity to humans.
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Affiliation(s)
- P A Rodrigues
- Department of Food Technology, Faculty of Veterinary, Molecular & Analytical Laboratory Center, Universidade Federal Fluminense, Niterói, Brazil
| | - R G Ferrari
- Department of Food Technology, Faculty of Veterinary, Molecular & Analytical Laboratory Center, Universidade Federal Fluminense, Niterói, Brazil.,Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - C A Conte-Junior
- Department of Food Technology, Faculty of Veterinary, Molecular & Analytical Laboratory Center, Universidade Federal Fluminense, Niterói, Brazil.,Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,National Institute of Health Quality Control, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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44
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Analysis of microbiota of the swimming crab (Portunus trituberculatus) in South Korea to identify risk markers for foodborne illness. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.08.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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45
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Ding ZF, Cao MJ, Zhu XS, Xu GH, Wang RL. Changes in the gut microbiome of the Chinese mitten crab (Eriocheir sinensis) in response to White spot syndrome virus (WSSV) infection. JOURNAL OF FISH DISEASES 2017; 40:1561-1571. [PMID: 28429823 DOI: 10.1111/jfd.12624] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 06/07/2023]
Abstract
Intestinal microorganisms play important roles in maintaining host health, but their functions in aquatic animal hosts have yet to be fully elucidated. The Chinese mitten crab, Eriocheir sinensis, is one such example. We attempted to identify the shift of gut microbiota that occurred in response to infection of white spot syndrome virus (WSSV), an emerging viral pathogen in the crab aquaculture industry. The microbiota may exert some control over aspects of the viral pathogenesis. We investigated the changes in composition and structure of the crab gut microbiome during various WSSV infection stages of 6 h post-infection (hpi) and 48 hpi, using a 16S rRNA approach on the MiSeq Illumina sequencing platform. Four phyla (Firmicutes, Proteobacteria, Tenericutes and Bacteroidetes) were most dominant in the gut of E. sinensis regardless of the WSSV infection stages. However, further analysis revealed that over 12 bacterial phyla, 44 orders and 68 families were significantly different in abundance at various states of WSSV infection. Several intriguing aspects of E. sinensis gut bacteria that had not been previously reported were also uncovered, such as class Mollicutes was dominant here, but absent in crabs from Yangtze River estuary and Chongming Islands. Overall, this study provided the first evidence that changes in gut microbiome were closely associated with the severity of WSSV infection and that indicator taxa could be used to evaluate the crab health status.
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Affiliation(s)
- Z F Ding
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Sciences and Chemistry, Jiangsu Second Normal University, Nanjing, China
| | - M J Cao
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Sciences and Chemistry, Jiangsu Second Normal University, Nanjing, China
| | - X S Zhu
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Sciences and Chemistry, Jiangsu Second Normal University, Nanjing, China
| | - G H Xu
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Sciences and Chemistry, Jiangsu Second Normal University, Nanjing, China
| | - R L Wang
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Sciences and Chemistry, Jiangsu Second Normal University, Nanjing, China
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46
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Chen CY, Chen PC, Weng FCH, Shaw GTW, Wang D. Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change. PLoS One 2017; 12:e0181427. [PMID: 28715471 PMCID: PMC5513549 DOI: 10.1371/journal.pone.0181427] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/22/2017] [Indexed: 11/18/2022] Open
Abstract
Growing evidence points out that the capacity of organisms to acclimate or adapt to new habitat conditions basically depends on their phenomic plasticity attributes, of which their gut commensal microbiota might be an essential impact factor. Especially in aquatic organisms, which are in direct and continual contact with the aquatic environment, the complex and dynamic microbiota have significant effects on health and development. However, an understanding of the relative contribution of internal sorting (host genetic) and colonization (environmental) processes is still unclear. To understand how microbial communities differ in response to rapid environmental change, we surveyed and studied the environmental and gut microbiota of native and habitat-exchanged shrimp (Macrobrachium nipponense) using 16S rRNA amplicon sequencing on the Illumina MiSeq platform. Corresponding with microbial diversity of their living water areas, the divergence in gut microbes of lake-to-river shrimp (CK) increased, while that of river-to-lake shrimp (KC) decreased. Importantly, among the candidate environment specific gut microbes in habitat-exchanged shrimp, over half of reads were associated with the indigenous bacteria in native shrimp gut, yet more candidates presented in CK may reflect the complexity of new environment. Our results suggest that shrimp gut microbiota has high plasticity when its host faces environmental changes, even over short timescales. Further, the changes in external environment might influence the gut microbiome not just by providing environment-associated microbes directly, but also by interfering with the composition of indigenous gut bacteria indirectly.
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Affiliation(s)
- Cheng-Yu Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Po-Cheng Chen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Francis Cheng-Hsuan Weng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | | | - Daryi Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail:
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47
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Troussellier M, Escalas A, Bouvier T, Mouillot D. Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity. Front Microbiol 2017; 8:947. [PMID: 28611749 PMCID: PMC5447324 DOI: 10.3389/fmicb.2017.00947] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 05/11/2017] [Indexed: 12/14/2022] Open
Abstract
Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism–microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.
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Affiliation(s)
- Marc Troussellier
- MARBEC, UMR IRD-CNRS-UM-IFREMER 9190, Université MontpellierMontpellier, France
| | - Arthur Escalas
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Thierry Bouvier
- MARBEC, UMR IRD-CNRS-UM-IFREMER 9190, Université MontpellierMontpellier, France
| | - David Mouillot
- MARBEC, UMR IRD-CNRS-UM-IFREMER 9190, Université MontpellierMontpellier, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, TownsvilleQLD, Australia
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48
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Shen H, Zang Y, Song K, Ma Y, Dai T, Serwadda A. A Meta-Transcriptomics Survey Reveals Changes in the Microbiota of the Chinese Mitten Crab Eriocheir sinensis Infected with Hepatopancreatic Necrosis Disease. Front Microbiol 2017; 8:732. [PMID: 28491058 PMCID: PMC5405120 DOI: 10.3389/fmicb.2017.00732] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/10/2017] [Indexed: 12/19/2022] Open
Abstract
Infection of the freshwater Chinese mitten crab Eriocheir sinensis with hepatopancreatic necrosis disease (HPND) has been a major problem in the crab-cultivated Chinese Province of Jiangsu since 2015. To explore the etiology of HPND, meta-transcriptomic libraries of the hepatopancreata from crabs with and without HPND were constructed. Comparison analyses showed that there were no statistically significant differences in viral and microsporidial communities in the hepatopancreata of diseased and healthy crabs. Bacteroidetes, Proteobacteria, and Firmicutes were the most dominant bacterial phyla in the hepatopancreata of healthy crabs, with a combined prevalence of 93%. However, a decrease in bacterial diversity and a striking shift in the microbial composition were found in the hepatopancreata of crabs infected with HPND. Tenericutes was the most prevalent bacterial phylum in diseased crabs (31.82%), whereas its prevalence was low in healthy crabs (0.02%). By contrast, the prevalence of Bacteroidetes was significantly lower in crabs with HPND (3.49%) than in crabs without HPND (41.04%). We also found that the prevalence of Actinobacteria was higher in crabs with HPND (16.70%) than in crabs without the disease (4.03%). The major bacterial family within the Tenericutes phylum in crabs with HPND was detected by polymerase chain reaction and determined to be Mycoplasmataceae. In conclusion, there were striking changes in the microbiota of diseased and healthy crabs. Specifically, the prevalence of bacteria belonging to Tenericutes and Actinobacteria phyla increased, whereas the prevalence of bacteria belonging to the Bacteroidetes phylum decreased in crabs with HPND, clearly pointing to an association with HPND.
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Affiliation(s)
- Huaishun Shen
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesWuxi, China.,Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Yanan Zang
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Kun Song
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Yuanchao Ma
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Tianhao Dai
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Ali Serwadda
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesWuxi, China.,Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
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49
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Gut Microbiota and Metabolic Phenotype of Portunus Trituberculatus. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60978-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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50
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Bouchon D, Zimmer M, Dittmer J. The Terrestrial Isopod Microbiome: An All-in-One Toolbox for Animal-Microbe Interactions of Ecological Relevance. Front Microbiol 2016; 7:1472. [PMID: 27721806 PMCID: PMC5033963 DOI: 10.3389/fmicb.2016.01472] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/05/2016] [Indexed: 12/12/2022] Open
Abstract
Bacterial symbionts represent essential drivers of arthropod ecology and evolution, influencing host traits such as nutrition, reproduction, immunity, and speciation. However, the majority of work on arthropod microbiota has been conducted in insects and more studies in non-model species across different ecological niches will be needed to complete our understanding of host–microbiota interactions. In this review, we present terrestrial isopod crustaceans as an emerging model organism to investigate symbiotic associations with potential relevance to ecosystem functioning. Terrestrial isopods comprise a group of crustaceans that have evolved a terrestrial lifestyle and represent keystone species in terrestrial ecosystems, contributing to the decomposition of organic matter and regulating the microbial food web. Since their nutrition is based on plant detritus, it has long been suspected that bacterial symbionts located in the digestive tissues might play an important role in host nutrition via the provisioning of digestive enzymes, thereby enabling the utilization of recalcitrant food compounds (e.g., cellulose or lignins). If this were the case, then (i) the acquisition of these bacteria might have been an important evolutionary prerequisite for the colonization of land by isopods, and (ii) these bacterial symbionts would directly mediate the role of their hosts in ecosystem functioning. Several bacterial symbionts have indeed been discovered in the midgut caeca of terrestrial isopods and some of them might be specific to this group of animals (i.e., Candidatus Hepatoplasma crinochetorum, Candidatus Hepatincola porcellionum, and Rhabdochlamydia porcellionis), while others are well-known intracellular pathogens (Rickettsiella spp.) or reproductive parasites (Wolbachia sp.). Moreover, a recent investigation of the microbiota in Armadillidium vulgare has revealed that this species harbors a highly diverse bacterial community which varies between host populations, suggesting an important share of environmental microbes in the host-associated microbiota. In this review, we synthesize our current knowledge on the terrestrial isopod microbiome and identify future directions to (i) fully understand the functional roles of particular bacteria (both intracellular or intestinal symbionts and environmental gut passengers), and (ii) whether and how the host-associated microbiota could influence the performance of terrestrial isopods as keystone species in soil ecosystems.
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Affiliation(s)
- Didier Bouchon
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers Poitiers, France
| | - Martin Zimmer
- Leibniz Center for Tropical Marine Ecology Bremen, Germany
| | - Jessica Dittmer
- Rowland Institute at Harvard, Harvard University, Cambridge MA, USA
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